Pacleb JM

References (2)

Title : Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence - Celniker_2002_Genome.Biol_3_RESEARCH0079
Author(s) : Celniker SE , Wheeler DA , Kronmiller B , Carlson JW , Halpern A , Patel S , Adams M , Champe M , Dugan SP , Frise E , Hodgson A , George RA , Hoskins RA , Laverty T , Muzny DM , Nelson CR , Pacleb JM , Park S , Pfeiffer BD , Richards S , Sodergren EJ , Svirskas R , Tabor PE , Wan K , Stapleton M , Sutton GG , Venter C , Weinstock G , Scherer SE , Myers EW , Gibbs RA , Rubin GM
Ref : Genome Biol , 3 :RESEARCH0079 , 2002
Abstract : BACKGROUND: The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were widely debated in the genomics community: how correct is the sequence with respect to base-pair (bp) accuracy and frequency of assembly errors? And, how difficult is it to bring a WGS sequence to the accepted standard for finished sequence? We are now in a position to answer these questions.
RESULTS: Our finishing process was designed to close gaps, improve sequence quality and validate the assembly. Sequence traces derived from the WGS and draft sequencing of individual bacterial artificial chromosomes (BACs) were assembled into BAC-sized segments. These segments were brought to high quality, and then joined to constitute the sequence of each chromosome arm. Overall assembly was verified by comparison to a physical map of fingerprinted BAC clones. In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps. We compared Release 3 to Release 2; in autosomal regions of unique sequence, the error rate of Release 2 was one in 20,000 bp.
CONCLUSIONS: The WGS strategy can efficiently produce a high-quality sequence of a metazoan genome while generating the reagents required for sequence finishing. However, the initial method of repeat assembly was flawed. The sequence we report here, Release 3, is a reliable resource for molecular genetic experimentation and computational analysis.
ESTHER : Celniker_2002_Genome.Biol_3_RESEARCH0079
PubMedSearch : Celniker_2002_Genome.Biol_3_RESEARCH0079
PubMedID: 12537568
Gene_locus related to this paper: drome-CG8058 , drome-CG9542 , drome-CG11309 , drome-CG11406 , drome-CG17097 , drome-CG17374 , drome-glita , drome-KRAKEN

Title : The genome sequence of Drosophila melanogaster - Adams_2000_Science_287_2185
Author(s) : Adams MD , Celniker SE , Holt RA , Evans CA , Gocayne JD , Amanatides PG , Scherer SE , Li PW , Hoskins RA , Galle RF , George RA , Lewis SE , Richards S , Ashburner M , Henderson SN , Sutton GG , Wortman JR , Yandell MD , Zhang Q , Chen LX , Brandon RC , Rogers YH , Blazej RG , Champe M , Pfeiffer BD , Wan KH , Doyle C , Baxter EG , Helt G , Nelson CR , Gabor GL , Abril JF , Agbayani A , An HJ , Andrews-Pfannkoch C , Baldwin D , Ballew RM , Basu A , Baxendale J , Bayraktaroglu L , Beasley EM , Beeson KY , Benos PV , Berman BP , Bhandari D , Bolshakov S , Borkova D , Botchan MR , Bouck J , Brokstein P , Brottier P , Burtis KC , Busam DA , Butler H , Cadieu E , Center A , Chandra I , Cherry JM , Cawley S , Dahlke C , Davenport LB , Davies P , de Pablos B , Delcher A , Deng Z , Mays AD , Dew I , Dietz SM , Dodson K , Doup LE , Downes M , Dugan-Rocha S , Dunkov BC , Dunn P , Durbin KJ , Evangelista CC , Ferraz C , Ferriera S , Fleischmann W , Fosler C , Gabrielian AE , Garg NS , Gelbart WM , Glasser K , Glodek A , Gong F , Gorrell JH , Gu Z , Guan P , Harris M , Harris NL , Harvey D , Heiman TJ , Hernandez JR , Houck J , Hostin D , Houston KA , Howland TJ , Wei MH , Ibegwam C , Jalali M , Kalush F , Karpen GH , Ke Z , Kennison JA , Ketchum KA , Kimmel BE , Kodira CD , Kraft C , Kravitz S , Kulp D , Lai Z , Lasko P , Lei Y , Levitsky AA , Li J , Li Z , Liang Y , Lin X , Liu X , Mattei B , McIntosh TC , McLeod MP , McPherson D , Merkulov G , Milshina NV , Mobarry C , Morris J , Moshrefi A , Mount SM , Moy M , Murphy B , Murphy L , Muzny DM , Nelson DL , Nelson DR , Nelson KA , Nixon K , Nusskern DR , Pacleb JM , Palazzolo M , Pittman GS , Pan S , Pollard J , Puri V , Reese MG , Reinert K , Remington K , Saunders RD , Scheeler F , Shen H , Shue BC , Siden-Kiamos I , Simpson M , Skupski MP , Smith T , Spier E , Spradling AC , Stapleton M , Strong R , Sun E , Svirskas R , Tector C , Turner R , Venter E , Wang AH , Wang X , Wang ZY , Wassarman DA , Weinstock GM , Weissenbach J , Williams SM , WoodageT , Worley KC , Wu D , Yang S , Yao QA , Ye J , Yeh RF , Zaveri JS , Zhan M , Zhang G , Zhao Q , Zheng L , Zheng XH , Zhong FN , Zhong W , Zhou X , Zhu S , Zhu X , Smith HO , Gibbs RA , Myers EW , Rubin GM , Venter JC
Ref : Science , 287 :2185 , 2000
Abstract : The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.
ESTHER : Adams_2000_Science_287_2185
PubMedSearch : Adams_2000_Science_287_2185
PubMedID: 10731132
Gene_locus related to this paper: drome-1vite , drome-2vite , drome-3vite , drome-a1z6g9 , drome-abhd2 , drome-ACHE , drome-b6idz4 , drome-BEM46 , drome-CG5707 , drome-CG5704 , drome-CG1309 , drome-CG1882 , drome-CG1986 , drome-CG2059 , drome-CG2493 , drome-CG2528 , drome-CG2772 , drome-CG3160 , drome-CG3344 , drome-CG3523 , drome-CG3524 , drome-CG3734 , drome-CG3739 , drome-CG3744 , drome-CG3841 , drome-CG4267 , drome-CG4382 , drome-CG4390 , drome-CG4572 , drome-CG4582 , drome-CG4851 , drome-CG4979 , drome-CG5068 , drome-CG5162 , drome-CG5355 , drome-CG5377 , drome-CG5397 , drome-CG5412 , drome-CG5665 , drome-CG5932 , drome-CG5966 , drome-CG6018 , drome-CG6113 , drome-CG6271 , drome-CG6283 , drome-CG6295 , drome-CG6296 , drome-CG6414 , drome-CG6431 , drome-CG6472 , drome-CG6567 , drome-CG6675 , drome-CG6753 , drome-CG6847 , drome-CG7329 , drome-CG7367 , drome-CG7529 , drome-CG7632 , drome-CG8058 , drome-CG8093 , drome-CG8233 , drome-CG8424 , drome-CG8425 , drome-CG9059 , drome-CG9186 , drome-CG9287 , drome-CG9289 , drome-CG9542 , drome-CG9858 , drome-CG9953 , drome-CG9966 , drome-CG10116 , drome-CG10163 , drome-CG10175 , drome-CG10339 , drome-CG10357 , drome-CG10982 , drome-CG11034 , drome-CG11055 , drome-CG11309 , drome-CG11319 , drome-CG11406 , drome-CG11598 , drome-CG11600 , drome-CG11608 , drome-CG11626 , drome-CG11935 , drome-CG12108 , drome-CG12869 , drome-CG13282 , drome-CG13562 , drome-CG13772 , drome-CG14034 , drome-nlg3 , drome-CG14717 , drome-CG15101 , drome-CG15102 , drome-CG15106 , drome-CG15111 , drome-CG15820 , drome-CG15821 , drome-CG15879 , drome-CG17097 , drome-CG17099 , drome-CG17101 , drome-CG17191 , drome-CG17192 , drome-CG17292 , drome-CG18258 , drome-CG18284 , drome-CG18301 , drome-CG18302 , drome-CG18493 , drome-CG18530 , drome-CG18641 , drome-CG18815 , drome-CG31089 , drome-CG31091 , drome-CG32333 , drome-CG32483 , drome-CG33174 , drome-dnlg1 , drome-este4 , drome-este6 , drome-GH02384 , drome-GH02439 , drome-glita , drome-KRAKEN , drome-lip1 , drome-LIP2 , drome-lip3 , drome-MESK2 , drome-nrtac , drome-OME , drome-q7k274 , drome-Q9VJN0 , drome-Q8IP31 , drome-q9vux3